After researching which of my special bridges should go where (never really got a good answer, but I have some good guesses) and making sure all the strings were the same tension (thank goodness for a tuning peg koto so I can do it myself.) I got the bridges in the right place for one of the many standard tunings and I'm thrilled! Since you can get the accidentals, you tune it so that all the notes are "valid" so anything you play sounds really awesome and Japanese. I picked out Sakura easily and with no problem. Plus the song book that came with it has sakura, so now I can backwards engineer the music a little bit.

I found some damage and I'm not sure if I did it or if was there to start with. It's just a bridge dent. A very bad picture to show how tall this thing is:

It's the whole mathmatics of string music. The last string's bridge is set almost at the end far from me, but because string octaves are halves and there are two octaves, you tend to eat up string length pretty fast. This image shows things from the top down. The arrows are pointing to the bridges.

The white things are the picks. You get different sounds when you pluck with fingers, use the picks. You can also hit and scrape with the picks as well.